High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection

Genome Research

Volumn 20, Issue 9, 2010, Pages 1288-1296

  Cooper, Sara J ^a   Finney, Gregory L ^a   Brown, Shauna L ^a   Nelson, Sven K ^a   Hesselberth, Jay ^a,c   MacCoss, Michael J ^a   Fields, Stanley ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL PROTEIN; RIBOSOME PROTEIN;

ARTICLE; BLACKFAN DIAMOND ANEMIA; CAPILLARY ELECTROPHORESIS; FUNGUS MUTANT; GENE DELETION; GENE EXPRESSION PROFILING; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

AMINO ACIDS; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; GENETIC VARIATION; METABOLOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 77956274547     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.105825.110     Document Type: Article

References (42)

1. Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB. 2003. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21: 692-696. (Pubitemid 36638098)
2. Blaise BJ, Giacomotto J, Elena B, Dumas ME, Toulhoat P, Segalat L, Emsley L. 2007. Metabotyping of Caenorhabditis elegans reveals latent phenotypes. Proc Natl Acad Sci 104: 19808-19812.
3. Caddick SE, Harrison CJ, Stavridou I, Johnson S, Brearley CA. 2007. A lysine accumulation phenotype of ScIpk2D mutant yeast is rescued by Solanum tuberosum inositol phosphate multikinase. Biochem J 403: 381-389. (Pubitemid 46706967)
4. Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, et al. 2004. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 32: D311-D314.
5. Edgar R, Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210. (Pubitemid 34679544)
6. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 95: 14863-14868. (Pubitemid 29003722)
7. Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ. 2008. Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data. Anal Chem 80: 961-971.
8. ForgacM. 1999. Structure and properties of the vacuolar (H+)-ATPases. J Biol Chem 274: 12951-12954.
9. Gatbonton T, Imbesi M, Nelson M, Akey JM, Ruderfer DM, Kruglyak L, Simon JA, Bedalov A. 2006. Telomere length as a quantitative trait: Genome-wide survey and genetic mapping of telomere length-control genes in yeast. PLoS Genet 2: e35. doi: 10.1371/journal.pgen.0020035.
10. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391. (Pubitemid 34826834)
11. Gieger C, Geistlinger L, Altmaier E, Hrabe de Angelis M, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, Adamski J, et al. 2008. Genetics meets metabolomics: A genome-wide association study of metabolite profiles in human serum. PLoS Genet 4: e1000282. doi: 10.1371/journal.pgen. 1000282.
12. Hibbs MA, Wallace G, Dunham M, Li K, Troyanskaya OG. 2008. Viewing the larger context of genomic data through horizontal integration. Proc IEEE Comput Sci 11th Int Conf Information Visualization 2008: 326-334.
13. Huang S, O'Shea EK. 2005. A systematic high-throughput screen of a yeast deletion collection for mutants defective in PHO5 regulation. Genetics 169: 1859-1871. (Pubitemid 40695603)
14. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, et al. 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25: 333-337. (Pubitemid 30437324)
15. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. 2003. Global analysis of protein localization in budding yeast. Nature 425: 686-691. (Pubitemid 37314307)
16. Humston EM, Dombek KM, Hoggard JC, Young ET, Synovec RE. 2008. Time-dependent profiling of metabolites from Snf1 mutant and wild type yeast cells. Anal Chem 80: 8002-8011.
17. Jauniaux JC, Vandenbol M, Vissers S, Broman K, Grenson M. 1987. Nitrogen catabolite regulation of proline permease in Saccharomyces cerevisiae. Cloning of the PUT4 gene and study of PUT4 RNA levels in wild-type and mutant strains. Eur J Biochem 164: 601-606. (Pubitemid 17072815)
18. Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30. (Pubitemid 30047706)
19. Kim Y, Ramirez-Montealegre D, Pearce DA. 2003. A role in vacuolar arginine transport for yeast Btn1p and for human CLN3, the protein defective in Batten disease. Proc Natl Acad Sci 100: 15458-15462. (Pubitemid 38021011)
20. Kind T, Wohlgemuth G , Lee DY, Lu Y, Palazoglu M, Shahbaz S, Fiehn O. 2009. FiehnLib: Mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 81: 10038-10048.
21. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, et al. 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
22. McGowan KA, Li JZ, Park CY, Beaudry V, Tabor HK, Sabnis AJ, Zhang W, Fuchs H, de AngelisMH, Myers RM, et al. 2008. Ribosomal mutations cause p53-mediated dark skin and pleiotropic effects. Nat Genet 40: 963-970.
23. Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S, Yasui A, van der Horst GT, Soga T, Ueda HR. 2009. Measurement of internal body time by blood metabolomics. Proc Natl Acad Sci 106: 9890-9895.
24. Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, et al. 2004. Exploration of essential gene functions via titratable promoter alleles. Cell 118: 31-44. (Pubitemid 38902812)
25. Mohler RE, Dombek KM, Hoggard JC, Young ET, Synovec RE. 2006. Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry analysis of metabolites in fermenting and respiring yeast cells. Anal Chem 78: 2700-2709.
26. Mohler RE, Tu BP, Dombek KM, Hoggard JC, Young ET, Synovec RE. 2008. Identification and evaluation of cycling yeast metabolites in two-dimensional comprehensive gas chromatography-time-of-flight-mass spectrometry data. J Chromatogr A 1186: 401-411.
27. Raamsdonk LM, Diderich JA, Kuiper A, van Gaalen M, Kruckeberg AL, Berden JA, Van Dam K. 2001a. Co-consumption of sugars or ethanol and glucose in a Saccharomyces cerevisiae strain deleted in the HXK2 gene. Yeast 18: 1023-1033. (Pubitemid 32780852)
28. Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ, et al. 2001b. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19: 45-50. (Pubitemid 32051955)
29. Robinson MD, De Souza DP, Keen WW, Saunders EC, McConville MJ, Speed TP, Likic VA. 2007. A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. BMC Bioinformatics 8: 419. doi: 10.1186/1471-2105-8-419.
30. Rochfort S. 2005. Metabolomics reviewed: A new "omics" platform technology for systems biology and implications for natural products research. J Nat Prod 68: 1813-1820.
31. Saldanha AJ. 2004. Java Treeview - extensible visualization of microarray data. Bioinformatics 20: 3246-3248. (Pubitemid 39619217)
32. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, et al. 2001. The Stanford Microarray Database. Nucleic Acids Res 29: 152-155.
33. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, et al. 2009. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457: 910-914.
34. Steffen KK, MacKay VL, Kerr EO, Tsuchiya M, Hu D, Fox LA, Dang N, Johnston ED, Oakes JA, Tchao BN, et al. 2008. Yeast life span extension by depletion of 60s ribosomal subunits is mediated by Gcn4. Cell 133: 292-302. (Pubitemid 351508304)
35. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, et al. 2001. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368. (Pubitemid 33140562)
36. Tsunoda M, Kato M, Fukushima T, Santa T, Homma H, Yanai H, Soga T, Imai K. 1999. Determination of aspartic acid enantiomers in bio-samples by capillary electrophoresis. Biomed Chromatogr 13: 335-339. (Pubitemid 29381287)
37. Vandenbol M, Jauniaux JC, Vissers S, Grenson M. 1987. Isolation of the NPR1 gene responsible for the reactivation of ammonia-sensitive aminoacid permeases in Saccharomyces cerevisiae. RNA analysis and gene dosage effects. Eur J Biochem 164: 607-612. (Pubitemid 17072816)
38. Villas-Boas SG, Hojer-Pedersen J, Akesson M, Smedsgaard J, Nielsen J. 2005. Global metabolite analysis of yeast: Evaluation of sample preparation methods. Yeast 22: 1155-1169. (Pubitemid 41684146)
39. Wang J, Alexander P, Wu L, Hammer R, Cleaver O, McKnight SL. 2009. Dependence of mouse embryonic stem cells on threonine catabolism. Science. 325, 435-439
40. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906. (Pubitemid 29381993)
41. Wishart DS. 2007. Human Metabolome Database: Completing the 'human parts list'. Pharmacogenomics 8: 683-686.
42. Zhu X, Shaw PN, Pritchard J, Newbury J, Hunt EJ, Barrett DA. 2005. Amino acid analysis by micellar electrokinetic chromatography with laser-induced fluorescence detection: Application to nanolitre-volume biological samples from Arabidopsis thaliana and Myzus persicae. Electrophoresis 26: 911-919. (Pubitemid 40430676)